Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin.
Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin.
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DOI：
10.1093/nar/gkw684
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发表时间：
2016-12-01
影响因子：
14.9
通讯作者：
Liu Y
中科院分区：
文献类型：
--
作者：
Xiong J;Gao S;Dui W;Yang W;Chen X;Taverna SD;Pearlman RE;Ashlock W;Miao W;Liu Y
纤毛虫原生动物嗜热四膜虫含有两种类型的结构和功能分化的细胞核：转录活性体细胞大核（MAC）和转录沉默种系微核（MIC）。在这里，我们证明 MAC 具有位于转录起始位点和侧翼剪接位点下游的核小体的良好位置。转录相关的反式决定簇促进 MAC 中核小体的定位。相比之下，MIC 中的核小体明显离域。尽管如此，MAC 和 MIC 中的核小体占用率彼此之间以及与基于 DNA 序列特征的体外重建和预测高度相关，揭示了顺式决定簇的出人意料的强大贡献。特别是，位置良好的核小体通常与 GC 含量振荡相匹配。由于许多核小体由顺式和反式决定簇协调容纳，我们认为它们的分布是由这些核小体对突变和转录景观的影响决定的，并由进化选择驱动。
The ciliate protozoan Tetrahymena thermophila contains two types of structurally and functionally differentiated nuclei: the transcriptionally active somatic macronucleus (MAC) and the transcriptionally silent germ-line micronucleus (MIC). Here, we demonstrate that MAC features well-positioned nucleosomes downstream of transcription start sites and flanking splice sites. Transcription-associated trans-determinants promote nucleosome positioning in MAC. By contrast, nucleosomes in MIC are dramatically delocalized. Nucleosome occupancy in MAC and MIC are nonetheless highly correlated with each other, as well as with in vitro reconstitution and predictions based upon DNA sequence features, revealing unexpectedly strong contributions from cis-determinants. In particular, well-positioned nucleosomes are often matched with GC content oscillations. As many nucleosomes are coordinately accommodated by both cis- and trans-determinants, we propose that their distribution is shaped by the impact of these nucleosomes on the mutational and transcriptional landscape, and driven by evolutionary selection.
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影响因子：
64.8
作者：
Brogaard, Kristin;Xi, Liqun;Wang, Ji-Ping;Widom, Jonathan
通讯作者：
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作者：
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